Complex Adaptive Systems
(M.Sc. in Bioinformatics, University of Athens)

Readings (2004)

Lecture 1. Introduction

FUNDAMENTAL

Introduction to the greek edition of Maturana & Varela's "Tree of knowledge", 1992 (by S.Manousselis).
PDF, 28 pages, 3501K
R.A.Brooks : Intelligence without representation, Artificial Intelligence Journal, 1991.
PDF, 12 pages, 712K
M.A.Bedau et al. : Open problems in artificial life, Artificial Life Journal, 2000.
PDF, 14 pages, 126K
M.A.Bedau : Artificial life, in "Blackwell Guide to the Philosophy of Computing and Information", by L.Floridi (Ed.), 2001.
PDF, 24 pages, 98K
P.Maes : Modeling adaptive autonomous agents, Artificial Life Journal, 1994.
PDF, 37 pages, 251K

ADDITIONAL

A.M.Turing : Computing machinery and intelligence, Mind 59:433-460, 1950.
PDF, 21 pages, 150K
R.A.Brooks : Intelligence without reason, Artificial Intelligence Memo 1293, MIT AI Lab, April 1991.
PDF, 28 pages, 342K
L.Steels : The artificial life roots of artificial intelligence, Artificial Life Journal, 1994.
PDF, 87 pages, 400K

Lecture 2. Behavioral models I (Navigation, control, regulation)

FUNDAMENTAL

V. Braitenberg : Vehicles, 1986 (chapters 1-7).
PDF, 31 pages, 4015K
D.McFarland : Animal behavior, 3rd edition, 1998 (chapters 24,25, animal economics & robotics).
PDF, 43 pages, 14632K
A.Guillot, J.-A.Meyer : The animat contribution to cognitive systems research, Journal of Cognitive Systems Research, 2000.
PDF, 8 pages, 60K
B.Webb, R.Harrison : Integrating sensorimotor systems in a robot model of cricket behaviour, SPIE Proceedings, 2000.
PDF, 12 pages, 309K

Lecture 3. Behavioral models II (Learning)

FUNDAMENTAL

D.Hebb : The organization of behavior, 1949 (introduction and chapter 4, growth of assembly, included in "Neurocomputing - Foundations of research" by Anderson & Rosenfeld, 1988).
PDF, 14 pages, 4562K
R.S.Sutton, A.G.Barto : Reinforcement learning - An introduction, 1998, (chapter 1, introduction).
PDF, 25 pages, 76K
D.McFarland : Animal behavior, 3rd edition, 1998 (chapter 17, conditioning & learning).
PDF, 15 pages, 2932K
O.Trullier et al. : Biologically-based artificial navigation systems - Review and prospects, Progress in Neurobiology, 1997.
PDF, 94 pages, 967K

ADDITIONAL

E.C.Tolman : Cognitive maps in rats and men, The Psychological Review, 55(4):189-208, 1948.
PDF, 14 pages, 237K
C.Balkenius : Spatial learning with perceptually grounded representations, Robotics and Autonomous systems, 25(1998):165-175.
PDF, 11 pages, 751K
T.Hartley, N.Burgess, C.Lever, F.Cacucci, J.O'Keefe : Modeling place fields in terms of the cortical inputs to the hippocampus, Hippocampus 10:369-379, 2000.
PDF, 11 pages, 434K
M.J.Mataric : Integration of representation into goal-driven behavior-based robots, IEEE Transactions on Robotics and Automation, 8(3):304-312, 1992.
PDF, 9 pages, 1747K
G.Beauchamp : Learning rules for social foragers: Implications for the producer-scrounger game and ideal-free distribution theory, Journal of Theoretical Biology, 207(2000):21-35.
PDF, 15 pages, 208K

Lecture 4. Populational models

FUNDAMENTAL

C.Reynolds : Flocks, herds and schools : A distributed behavioral model, SIGGRAPH-87, 21(4).
PDF, 13 pages, 120K
R.Durrett, S. Levin : The importance of being discrete (and spatial), Theoretical Population Biology, 46:363-394, 1994.
PDF, 32 pages, 1162K
W.G.Wilson : Lotka's game in predator-prey theory : Linking populations to individuals, Theoretical Population Biology, 50:368-393, 1996.
PDF, 26 pages, 2040K
J.Schull : Are species intelligent?, Behavioral and Brain Sciences, 13:63-108, 1990.
PDF, 28 pages, 3526K

ADDITIONAL

R.Schoonderwoerd, O.Holland, J.Bruten, L.Rothkrantz : Ant-based load balancing in telecommunication networks, Adaptive Behavior Journal, 5(2):169-207, 1997.
PDF, 26 pages, 152K

Lecture 5. Evolutionary models I (Techniques)

FUNDAMENTAL

M.Mitchell : An introduction to genetic algorithms, MIT Press, 1996 (chapter 1 : general overview).
PDF, 34 pages, 8912K
J.Koza : Genetic evolution and co-evolution of computer programs, Proceedings Artificial Life II, 1990.
PDF, 33 pages, 190K
Z.Michalewicz, R.Hinterding, M.Michalewicz : Evolutionary algorithms, Chapter 2 in Fuzzy Evolutionary Computation, W.Pedrycz (editor), Kluwer Academic, 1997.
PDF, 29 pages, 324K
R.D.Beer, R.D.Quinn, H.J.Chiel, R.E.Ritzmann : Biologically inspired approaches to robotics, Communications of the ACM, 40(3):30-38, March 1997.
PDF, 9 pages, 1157K

ADDITIONAL

M.Dorigo, G.DiCaro, L.M.Gambardella : Ant algorithms for discrete optimization, Journal of Artificial Life, 1999.
PDF, 36 pages, 339K
P.Husbands, I.Harvey, D.Cliff, G.Miller : Artificial evolution - A new path for artificial intelligence?, Brain and Cognition, 34(1997):130-159.
PDF, 30 pages, 909K
S.Nolfi : Learning and evolution in neural networks, in M. A.Arbib (Ed.), Handbook of brain theory and neural networks, Second Edition. Cambridge, MA: MIT Press, pp.415-418..
PDF, 8 pages, 30K
S.Nolfi, D.Parisi : Evolution of artificial neural networks, in M. A.Arbib (Ed.), Handbook of brain theory and neural networks, Second Edition. Cambridge, MA: MIT Press, pp.418-421.
PDF, 8 pages, 41K

Lecture 6. Evolutionary models II (Populational phenomena)

FUNDAMENTAL

R.Dawkins : The selfish gene, Oxford University Press, 1976 (chapter 1 : What is man ?, chapter 11 : Memes, the new replicators, greek translation)
Chapter 1, PDF, 11 pages, 2400K
Chapter 11, PDF, 12 pages, 3280K
P.Turney : Myths and legends of the Baldwin effect, Proceedings of the Workshop on "Evolutionary Computation and Machine Learning", 13th International Conference on Machine Learning, Bari, Italy, 1996.
PDF, 8 pages, 33K
T.S.Ray : An evolutionary approach to synthetic biology - Zen and the art of creating life, Artificial Life Journal, 1994.
PDF, 39 pages, 271K
S.A.L.M.Kooijman, P.Auger, J.C.Poggiale, B.W.Kooi : Quantitative steps in symbiogenesis and the evolution of homeostasis, Biol.Rev. 2003.
PDF, 29 pages, 404K
U. Dieckmann, M. Doebeli : On the origin of species by sympatric speciation, Nature, 400(6742):311-2, Jul 22 1999.
PDF, 19 pages, 486K

ADDITIONAL

J.M.Baldwin : A new factor in evolution, American Naturalist 30, pages 441-451 and 536-553, June 1896.
PDF, 20 pages, 95K

G.E.Hinton, S.J.Nowlan : How learning can guide evolution, Complex Systems, 1(1987):495-502.
PDF, 5 pages, 104K

Memetics website
http://www.ing.unlp.edu.ar/cetad/mos/memetic_home.html

Lecture 7. Evolutionary models III (Games and cooperation)

FUNDAMENTAL

R.Axelrod, W.Hamilton : The evolution of cooperation in biological systems, chapter 5 in "The Evolution of Cooperation", by R.Axelrod, Basic Books, 1984.
PDF, 10 pages, 2670K
J.R.Krebs, N.B.Davies : An introduction to behavioural ecology, (chapter 11: On selfishness and altruism), 3rd Edition, Blackwell, 1993.
PDF, 26 pages, 7052K
R.Hoffmann : Twenty years on : The evolution of cooperation revisited, Journal of Artificial Societies and Social Simulation, 3(2), March 2000.
PDF, 13 pages, 159K
E.S.Tzafestas : Spatial games with adaptive tit-for-tats, Proceedings of the 6th "Parallel Problem Solving from Nature" (PPSN-VI), Paris, September 2000.
PDF, 10 pages, 115K
T.N.Sherratt, G.Roberts : The stability of cooperation under variable investment, Journal of Theoretical Biology, 215:47-56, 2002.
PDF, 10 pages, 213K
L.A.Dugatkin : Cooperation in animals : An evolutionary overview, Biology and Philosophy, 17:459-476, 2002.
PDF, 18 pages, 317K

Lecture 8. Molecular models

FUNDAMENTAL

L.Raeymaekers : Dynamics of boolean networks controlled by biologically meaningful functions, Journal of Theoretical Biology, 218:331-341, 2002.
PDF, 11 pages, 160K
R.V.Sole, R.Pastor-Satorras : Complex networks in genomics and proteomics, In: Handbook of Graphs and Networks, S. Bornholdt & H. G. Schuster (eds.), John Wiley-VCH, 2002.
PDF, 25 pages, 694K
O.Wolkenhauer, H.Kitano, K-H.Cho : An introduction to systems biology, IEEE Control Systems Magazine, Vol.23, No.4, 38-48, August 2003.
PDF, 14 pages, 238K
W.Fontana, L.W.Buss: What would be conserved if "the tape were played twice"?, Proceedings of the National Academy of Sciences (USA), Vol.91, 757-761, January 1994.
PDF, 5 pages, 1150K

ADDITIONAL

I.Shmulevich, E.Dougherty, S.Kim, W.Zhang : Probabilistic boolean networks - A rule-based uncertainty model for gene regulatiry networks, Bioinformatics 18(2):261-274, 2002.
PDF, 14 pages, 198K

H.Baltscheffsky, C.Blomberg, H.Liljenstroem, B.I.B.Lindahl, P.Arhem : On the origin and evolution of life - An introduction, Journal of Theoretical Biology, 187(1997):453-459.
PDF, 7 pages, 153K

L.Varetto : Studying artificial life with a molecular automaton, Journal of Theoretical Biology, 193(1998):257-285.
PDF, 29 pages, 508K

Journal of Theoretical Biology, Special issue on Metabolic Control Vol. 182, Issue 3, 7 October 1996.
Available online from Science Direct

Lecture 9. Developmental models I (Structures and forms)

FUNDAMENTAL

P.Agarwal : Cellular segregation and engulfment simulations using the Cell Programming Language, Journal of Theoretical Biology, 176(1995):79-89.
PDF, 11 pages, 1290K
C.Furusawa, K.Kaneko : Emergence of rules in cell society : Differentiation, Hierarchy and Stability, Bulletin of Mathematical Biology, 60:659-687, 1998.
PDF, 29 pages, 1245K
R.J.De Boer, A.A.Freitas, A.S.Perelson : Resource competition determines selection of B cell repertoires, Journal of Theoretical Biology, 212(2001):333-343.
PDF, 11 pages, 313K
P.Prusinkiewicz, M.Hammel, J.Hana, R.Mech: Visual models of plant development, In: Handbook of Formal Languages, by G.Rozenberg and A.Salomaa (Eds.), Springer Verlag, 1996.
PS, 49 pages, 7645K

ADDITIONAL

A.Cangelosi, D.Parisi, S.Nolfi : Cell division and migration in a 'genotype' for neural networks, Network, 5:497-515, 1994.
PDF, 25 pages, 126K
A.M.Turing : The chemical basis of morphogenesis, Philosophical Transactions of the Royal Society of London, Series B (Biological Sciences), Volume 237, Issue 641, pages 37-72, August 1952.
PDF, 37 pages, 5356K

Lecture 10. Developmental models II (Fractals)

FUNDAMENTAL

J.Lin : Fractal Image Coding, Course Slides ECE 447, Univ. of Illinois at Urbana Champaign.
PDF, 33 pages, 1160K

Lecture 11. Cellular automata

FUNDAMENTAL

N.Packard, S.Wolfram : Two-dimensional cellular automata, Journal of Statistical Physics, 38:901-946, March 1985.
PDF, 51 pages, 890K

Lecture 12. Dynamical systems

FUNDAMENTAL

K.McCann, A.Hastings, S.Harrison, W.Wilson : Population outbreaks in a discrete world, Theoretical Population Biology, 57(2):97-108, March 2000.
PDF, 12 pages, 290K
P.A.Abrams, C.E.Brassil, R.D.Holt : Dynamics and responses to mortality rates of competing predators unergoing predator-prey cycles, Theoretical Population Biology, 64(2):163-176, September 2003.
PDF, 14 pages, 500K

Page last updated 08 July 2004.
Send me mail (brensham@softlab.ece.ntua.gr)

Complex Adaptive Systems (M.Sc. in Bioinformatics, University of Athens)

Readings (2004)

Lecture 1. Introduction

Lecture 3. Behavioral models II (Learning)

Lecture 6. Evolutionary models II (Populational phenomena)

Lecture 7. Evolutionary models III (Games and cooperation)

Complex Adaptive Systems
(M.Sc. in Bioinformatics, University of Athens)